On Fri, Oct 19, 2012 at 05:27:25PM +0200, Edward d'Auvergne wrote:
> Hi,
>
> This is now another problem which I haven't encountered because none
> of my test systems (Mac OS X 10.6 and 10.7, MS Windows 2000 and 7, and
> GNU/Linux (with Python 2.3, 2.4, 2.5, 2.6, 2.7, 3.1, 3.2, and 3.3))
> have the Scientific Python module installed anymore. I'll have to
> play with this on the weekend. This new issue is the VMD interfacing
> via Scientific Python. I would suggest changing the Scientific Python
> VMD section from the dep_check.py file. I.e. on line 160 from:
>
> "except ImportError:"
>
> to:
>
> "except:"
>
> as a work around. I might have to report this as a numpy bug - from
> all the reports I can now clearly see that that is where the broken
> code is - but also have relax work around it. I hope you don't see
> any other problems.
>
> Cheers,
>
> Edward
Edward,
Thanks, that additional change was sufficient, with the other two patches,
to allow relax 2.1.2 to build
under fink. I'll just add those to the relax-py.patch for now and use the
existing relax 2.1.2 tarball.
Jack
>
>
>
>
> On 19 October 2012 17:13, Jack Howarth <[email protected]> wrote:
> > On Fri, Oct 19, 2012 at 04:54:21PM +0200, Edward d'Auvergne wrote:
> >> Hi Jack,
> >>
> >> I noticed this one too late. It is a very, very strange error! The
> >> problem is scipy: it's a bit of a wild mix of crazy code which tends
> >> to do a lot of weird low level things to Python. In this case, I
> >> traced the problem back to a change which only affected the import of
> >> the ctypes Python module. I really don't know how slightly changing a
> >> ctypes import statement would trigger a bug in scipy - that is
> >> bizarre. I fixed it after branching relax 2.1.2 at:
> >>
> >> http://article.gmane.org/gmane.science.nmr.relax.scm/15667
> >> http://article.gmane.org/gmane.science.nmr.relax.scm/15668
> >>
> >> There are two options, the change at r17912
> >> (http://article.gmane.org/gmane.science.nmr.relax.scm/15668) should be
> >> sufficient and could be ported to the 2.1.2 code. Or I could release
> >> 2.1.3 with just this change and only release the source tar.bz2 file
> >> for fink. Which option is easiest for you?
> >>
> >> Cheers,
> >>
> >> Edward
> >
> > Edward,
> > Neither http://article.gmane.org/gmane.science.nmr.relax.scm/15668 or
> > it in combination with
> > http://article.gmane.org/gmane.science.nmr.relax.scm/15667
> > appear to be sufficient to eliminate the error here...
> >
> > /sw/bin/python2.7 /sw/bin/scons
> > scons: Reading SConscript files ...
> > AttributeError: 'builtin_function_or_method' object has no attribute
> > 'dispatch':
> > File "/sw/src/fink.build/relax-py27-2.1.2-1/relax-2.1.2/SConstruct", line
> > 37:
> > from scons.distrib import package, gpg_sign
> > File
> > "/sw/src/fink.build/relax-py27-2.1.2-1/relax-2.1.2/scons/distrib.py", line
> > 32:
> > from version import version
> > File "/sw/src/fink.build/relax-py27-2.1.2-1/relax-2.1.2/version.py", line
> > 26:
> > import dep_check
> > File "/sw/src/fink.build/relax-py27-2.1.2-1/relax-2.1.2/dep_check.py",
> > line 157:
> > from Scientific.Visualization import VMD # This requires Numeric to
> > be installed (at least in Scientific 2.7.8).
> > File "/sw/lib/python2.7/site-packages/Scientific/Visualization/VMD.py",
> > line 40:
> > from Scientific.Geometry import Transformation, Vector, ex, ey, ez
> > File "/sw/lib/python2.7/site-packages/Scientific/Geometry/__init__.py",
> > line 25:
> > import Scientific_vector
> > File "Scientific_vector.pyx", line 13:
> > None
> > File "/sw/lib/python2.7/site-packages/Scientific/N.py", line 15:
> > from numpy.oldnumeric import *
> > File "/sw/lib/python2.7/site-packages/numpy/oldnumeric/__init__.py", line
> > 14:
> > from compat import *
> > File "/sw/lib/python2.7/site-packages/numpy/oldnumeric/compat.py", line
> > 106:
> > class Unpickler(pickle.Unpickler):
> > File "/sw/lib/python2.7/site-packages/numpy/oldnumeric/compat.py", line
> > 110:
> > dispatch = copy.copy(pickle.Unpickler.dispatch)
> >
> > Jack
> >>
> >>
> >>
> >> On 19 October 2012 16:00, Jack Howarth <[email protected]> wrote:
> >> > Edward,
> >> > While trying to update the current fink relax-py packaging to the new
> >> > 2.1.2 release.
> >> > I ran into a build failure of the form...
> >> >
> >> > /sw/bin/python2.7 /sw/bin/scons
> >> > scons: Reading SConscript files ...
> >> > AttributeError: 'builtin_function_or_method' object has no attribute
> >> > 'dispatch':
> >> > File "/sw/src/fink.build/relax-py27-2.1.2-1/relax-2.1.2/SConstruct",
> >> > line 37:
> >> > from scons.distrib import package, gpg_sign
> >> > File
> >> > "/sw/src/fink.build/relax-py27-2.1.2-1/relax-2.1.2/scons/distrib.py",
> >> > line 32:
> >> > from version import version
> >> > File "/sw/src/fink.build/relax-py27-2.1.2-1/relax-2.1.2/version.py",
> >> > line 26:
> >> > import dep_check
> >> > File "/sw/src/fink.build/relax-py27-2.1.2-1/relax-2.1.2/dep_check.py",
> >> > line 143:
> >> > import scipy
> >> > File "/sw/lib/python2.7/site-packages/scipy/__init__.py", line 85:
> >> > from numpy import oldnumeric
> >> > File "/sw/lib/python2.7/site-packages/numpy/oldnumeric/__init__.py",
> >> > line 14:
> >> > from compat import *
> >> > File "/sw/lib/python2.7/site-packages/numpy/oldnumeric/compat.py",
> >> > line 106:
> >> > class Unpickler(pickle.Unpickler):
> >> > File "/sw/lib/python2.7/site-packages/numpy/oldnumeric/compat.py",
> >> > line 110:
> >> > dispatch = copy.copy(pickle.Unpickler.dispatch)
> >> >
> >> > This failure didn't occur with the relax 2.1.0 or 2.1.1 releases.
> >> > Interestingly this
> >> > error looks like the one described in the thread...
> >> >
> >> > http://scons.tigris.org/ds/viewMessage.do?dsForumId=1272&dsMessageId=2695657
> >> >
> >> > Jack
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